Scientists recently gifted the wheat industry something important in the form of a database.

The bespoke data was generated by an international consortium that undertook a deep analysis of contrasting wheat genomes. This involved fully sequencing the genomes of 15 significant wheat cultivars from global breeding programs, including two Australian varieties – AGT Mace and LRPB Lancer.

The comparison allowed genetic differences to pop out across the entire genome. In turn, this provides a new framework to understand decades of accumulated crop performance data, a feat that will transform how (and how quickly) high-performing cultivars are bred in the future via selection for valuable genetic differences across the entire genome.

The global project was undertaken with a great deal of Australian input that was enabled by investment from GRDC through a project called the 10+ Genome Wheat Sequencing Consortium.

Originally headed by Professor Peter Langridge – who was a key international driver with Curtis Pozniak in Canada – the GRDC project was completed with Associate Professor Ken Chalmers at the helm. Both are based at the University of Adelaide.

Associate Professor Chalmers says the new database creates an unprecedented ability to compare and contrast wheat genomes, a feature that elevates the predictive power of genomics to a new level.

“We can now see that there is a core set of genes present in every wheat cultivar alongside genes that are present only in some,” Associate Professor Chalmers says. “It is the latter set of genes that are implicated in region-specific adaptations to growing conditions, including traits that are important to productivity, such as disease resistance, tolerance to environmental stresses and even grain quality.”

The data reveals a genome that has undergone extensive structural rearrangements, including the appearance of large chunks of DNA derived from wild relatives and differences in gene content resulting from complex breeding histories. Among the genetic variation that influences agronomically important traits, the consortium detected:

• single-nucleotide polymorphisms (SNPs);
• DNA insertions or deletions (indels);
• variation in the presence or absence (PAV) of genes, which affected about 12 per cent of all genes in the genome; and
• gene copy number variation (CNV), which affected about 26 per cent of genes indicating that CNV is a strong contributor to genetic variation in wheat.

The total number of projected genes ranged between 118,734 and 120,967.

Standout examples of agronomically important genetic elements included:

• identification of a gene (called Sm1) that provides resistance to the orange wheat blossom midge through a similar class of molecules as a stem rust resistance gene (Rpg5); and
• genes that could be used in hybrid breeding programs to restore fertility.

In communicating the findings in the scientific literature, the authors concluded that:

“These genome assemblies will provide a basis for functional gene discovery and breeding to deliver the next generation of modern wheat cultivars.”

Importantly, the consortium also drove technological advancements, including reducing the amount of time needed to fully sequence the wheat genome from five years, when it was first attempted, down to a couple of weeks. The cost has also been reduced.

“Bread wheat is among the biggest of the genomes sequenced and it represents one of the biggest challenges in terms of assembling the DNA sequence in the correct order,” Associate Professor Chalmers says.

“That’s because wheat combines the genomes of three ancestral grasses. Each of these three genomes contains seven chromosomes that possess overarching similarities. We can now rapidly assemble the sequence thanks to advances we made in bioinformatics.”

The wheat cultivars sequenced were selected through a process that allowed participating nations to nominate one or two cultivars. In Australia, the selection was made at a meeting of wheat breeders, with AGT Mace and LRPB Lancer selected to provide coverage of the main Australian wheat growing regions.

Other participating nations included the UK, the US, European Union countries, Canada, China, Israel, Switzerland, Saudi Arabia and Japan, as well as the International Maize and Wheat Improvement Center in Mexico.

Also taking part in Australia beside the University of Adelaide was the Centre for AgriBioscience in Victoria.

The 10+ Genome Wheat Sequencing database is now publicly available worldwide, with open access designed to help drive improvements in wheat crop performance.

More information: Ken Chalmers, ken.chalmers@adelaide.edu.au